We've been noticing similar masking issues with our non-HCP data acquired on a GE MR750, and have found that fat sat in our sequence was turned off, so we will attempt to do the same and report whether that changes things.
__________________________ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Dec 1, 2016, at 2:01 PM, Julien Dubois wrote: > It looks like the Freesurfer pipeline does not make use of the MNI space > registration from the last Prefreesurfer step. > Hence, to correct for the suboptimal MNI registration due to the fat sat > discrepancy, my plan of action is to: > 1) generate a "no fat sat" T1w template > 2) re-run AtlasRegistrationToMNI152_FLIRTandFNIRT.sh (last step of the > PreFreesurfer pipeline) > 3) re-run the PostFreesurfer pipeline > Does that sound reasonable? > > If 2) doesn't work well, I'll look into using the T2w image for MNI space > registration instead. > > - Julien > > > Julien Dubois, PhD > Postdoctoral Scientist > Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles > Department of the Humanities and Social Sciences, California Institute of > Technology, Pasadena > Tel: +1 (310)423-8377 > Web: http://nigiri.caltech.edu/~jdubois > > > On Thu, Dec 1, 2016 at 10:24 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > If you have a decent number of subjects that go through the pipelines okay, > you can just generate another average template after MNI registration. Else, > there isn’t any particular reason why a T1w-based MNI registration is better > than a T2w-based registration. We probably should make a flag that > automatically allows you to base the brain mask and atlas registration on the > T2w image. > > Peace, > > Matt. > > From: Julien Dubois <jcrdub...@gmail.com> > Date: Thursday, December 1, 2016 at 11:49 AM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Distorted MNI space result (T?w_restore) -- maybe > due to "bad" initial brain mask? > > Thank you Matt. > > I actually don't think the brain extraction is the culprit, after spending > more time with the intermediate outputs. Indeed, > T1w/T1w_acpc_dc_restore_brain.nii.gz actually looks quite good. > > The issue mostly arises at the fnirt step in > AtlasRegistrationToMNI152_FLIRTandFNIRT.sh. And indeed, it is clear that the > template from the HCP pipelines (MNI152_T1_2mm.nii.gz) is very dark between > the brain and the skull, while my input image > (T1w/T1w_acpc_dc_restore.nii.gz) is not. The best solution will thus consist > in using a template with fat sat off. > > Any idea where I might find such a template? I'll look around, but if you > have suggestions, let me know. > > - Julien > > Julien Dubois, PhD > Postdoctoral Scientist > Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles > Department of the Humanities and Social Sciences, California Institute of > Technology, Pasadena > Tel: +1 (310)423-8377 > Web: http://nigiri.caltech.edu/~jdubois > > > On Wed, Nov 30, 2016 at 5:41 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > If you had a volume template in MNI space that had fat sat off, it might > register better. Alternatively you might modify the pipelines to use the > brain mask from the T2w scan and to do the atlas registration from the T2w > scan. > > Peace, > > Matt. > > From: Julien Dubois <jcrdub...@gmail.com> > Date: Wednesday, November 30, 2016 at 5:51 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Distorted MNI space result (T?w_restore) -- maybe > due to "bad" initial brain mask? > > I am not sure -- I am checking with the people who acquired that data. > I have had similar issues before with in-house data which does not have fat > sat turned on. > Do you recommend a tweak to the PreFreeSurfer pipeline if fat sat is not > turned on? > > I now see that you recommmend fat sat in the HCP T1 protocol [“Fat suppr. = > Water excit. Fast”] to reduce signal from bone marrow and scalp fat > > - Julien > > Julien Dubois, PhD > Postdoctoral Scientist > Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles > Department of the Humanities and Social Sciences, California Institute of > Technology, Pasadena > Tel: +1 (310)423-8377 > Web: http://nigiri.caltech.edu/~jdubois > > > On Wed, Nov 30, 2016 at 2:18 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Out of curiosity, does this data not have fat sat on the T1w scan? > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Julien Dubois > <jcrdub...@gmail.com> > Date: Wednesday, November 30, 2016 at 2:51 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Distorted MNI space result (T?w_restore) -- maybe due to > "bad" initial brain mask? > > Dear Matt > > I am processing some non-HCP data with the minimal pipelines (v3.5.0). I > don't think that the problem that I am encountering is due to using an older > version of the Pipelines. > > I just looked at one of the subjects, and the MNI normalized T?w_restore > (under MNINonLinear/) are quite distorted (though the initial brain was > perfectly good looking). In particular, the left parietal area is "cut", as > per this screenshot showing the resulting T2w_restore overlaid on the 1mm > template ("${HCPPIPEDIR_Templates}/MNI152_T2_1mm.nii.gz") > > <image.png> > > Upon inspecting the various outputs generated during PreFreesurfer, I can see > that the initial brain mask includes some non-brain matter in the left > parietal cortex (screenshot below) . This might be the source of the > distorted output. How can I solve this issue? > <image.png> > > My input T1w & T2w are 1mm isotropic and I am using the 1mm templates. I am > not applying gradient non-linearity or distortion correction. > > > All the files generated by the Pipelines (PreFS, FS, and PostFS) are > available here, and so are the two screenshots if they don't show up properly > in this email. > > Thank you in advance for your help, > - Julien > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
